Killing Experiments

This notebook is the settings used to run the simulations with tumor_tcell_ABM to compare to the in vitro experimental data

Load Packages

#Experiment tumor-tcell modules needed
from tumor_tcell.experiments.killing_experiments import killing_experiment
from tumor_tcell.library.population_plots import cytotoxicity_rep_plot
import warnings
warnings.filterwarnings('ignore')

Loading chipmunk for Linux (64bit) [/mnt/c/Users/akoya-stanford/Python_Code/tumor-tcell/vivarium_env/lib/python3.8/site-packages/pymunk/libchipmunk.so]

killing_experiment, takes as arguments:

• N_cells, the number of cells to use for the simulation
• save_name, the same to save the experimental output with
• num_rep, the number of replicates
• tumor_t_raio, the ratio of tumor to T cells to be used This starts this tumor_tcell_experiments for conditions of T cells to different percentages of PDL1+ tumors cells and no T cell controls, performs the replicates, and processes the data for each

killing_experiment(N_cells=55,save_name='2_1rep', num_rep=2, tumor_t_ratio=2)

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killing_experiment(N_cells=55,save_name='4', num_rep=2)

Do analysis for the replicates

cytotoxicity_rep_plot takes the killing_experimental output and processes it for statistics and creates plots that summarize the cytotoxicity for the experiments

cytotoxicity_rep_plot(num_rep=2,save_name='2_1rep')

cytotoxicity_rep_plot(num_rep=5,save_name='4')